Changeset b73545

Timestamp:

Sep 15, 2014, 2:28:50 PM (10 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

7f1b51

Parents:

55736b (diff), 5524ae9 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'MemFixes' into stable

Conflicts:

src/Tesselation/boundary.cpp

• Lots of functions removed in boundary.cpp in Cleanup_old_code but seemingly also affected during MemFixes.

Files:

• LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (modified) (1 diff)
• LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp (modified) (1 diff)
• LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.hpp (modified) (1 diff)
• LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (modified) (3 diffs)
• src/Actions/ActionQueue.cpp (modified) (5 diffs)
• src/Actions/ActionQueue.hpp (modified) (4 diffs)
• src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) (2 diffs)
• src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) (1 diff)
• src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) (1 diff)
• src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) (1 diff)
• src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) (1 diff)
• src/Actions/CommandAction/ElementDbAction.cpp (modified) (2 diffs)
• src/Actions/PotentialAction/FitPotentialAction.cpp (modified) (1 diff)
• src/Actions/Process.cpp (modified) (1 diff)
• src/Analysis/analysis_correlation.cpp (modified) (5 diffs)
• src/Box.cpp (modified) (1 diff)
• src/Box.hpp (modified) (1 diff)
• src/Fragmentation/Exporters/SaturationDistanceMaximizer.cpp (modified) (2 diffs)
• src/Fragmentation/Homology/HomologyContainer.hpp (modified) (1 diff)
• src/LinkedCell/linkedcell.cpp (modified) (2 diffs)
• src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) (1 diff)
• src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) (1 diff)
• src/Parser/PdbParser.cpp (modified) (1 diff)
• src/Potentials/PartialNucleiChargeFitter.cpp (modified) (3 diffs)
• src/Potentials/PotentialRegistry.cpp (modified) (1 diff)
• src/Potentials/PotentialRegistry.hpp (modified) (1 diff)
• src/Potentials/SerializablePotential.hpp (modified) (1 diff)
• src/Tesselation/CandidateForTesselation.cpp (modified) (1 diff)
• src/Tesselation/tesselation.cpp (modified) (2 diffs)
• src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) (2 diffs)
• src/World.cpp (modified) (1 diff)
• src/builder.cpp (modified) (1 diff)
• src/cleanUp.cpp (modified) (2 diffs)
• src/documentation/tests/tests.dox (modified) (3 diffs)
• tests/regression/Atoms/Add/testsuite-atoms-add.at (modified) (1 diff)
• tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (modified) (3 diffs)
• tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (modified) (3 diffs)

LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp

@@ -88 +88 @@
 MatrixContent::MatrixContent(size_t _rows, size_t _columns, MatrixBaseCase) :
     MatrixDimension(_rows,_columns),
-    free_content_on_exit(true)
+    free_content_on_exit(false)
 {}
 

LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp

@@ -189 +189 @@
   {
     ar & boost::serialization::base_object<MatrixDimension>(*this);
+    if (free_content_on_exit)
+      gsl_matrix_free(content);
     content = gsl_matrix_calloc(getRows(), getColumns());
     ar & content->size1;

LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.hpp

@@ -179 +179 @@
   void save(Archive & ar, const unsigned int version) const
   {
-    ar & content;
+    ar & *content;
   }
   template<class Archive>
   void load(Archive & ar, const unsigned int version)
   {
-    ar & content;
-    createViews();
+    ar & *content;
   }
   BOOST_SERIALIZATION_SPLIT_MEMBER()

LinearAlgebra/src/LinearAlgebra/VectorContent.cpp

@@ -55 +55 @@
   VectorDimension(0),
   content(NULL),
-  free_content_on_exit(true)
+  free_content_on_exit(false)
 {}
 
@@ -78 +78 @@
 VectorContent::VectorContent(VectorBaseCase) :
     VectorDimension(0),
+    content(NULL),
     free_content_on_exit(false)
 {}
@@ -112 +113 @@
 VectorContent::VectorContent(const size_t _dimension, std::istream &inputstream) :
   VectorDimension(_dimension),
-  content(NULL),
   free_content_on_exit(true)
 {

src/Actions/ActionQueue.cpp

@@ -74 +74 @@
 #endif
 
-  // free all actions contained in actionqueue
-  for (ActionQueue_t::iterator iter = actionqueue.begin(); !actionqueue.empty(); iter = actionqueue.begin()) {
-    delete *iter;
-    actionqueue.erase(iter);
-  }
+  clearQueue();
 
   delete history;
@@ -86 +82 @@
 void ActionQueue::queueAction(const std::string &name, enum Action::QueryOptions state)
 {
-  queueAction(AR->getActionByName(name), state);
-}
-
-void ActionQueue::queueAction(Action *_action, enum Action::QueryOptions state)
+  const Action * const registryaction = AR->getActionByName(name);
+  queueAction(registryaction, state);
+}
+
+void ActionQueue::queueAction(const Action * const _action, enum Action::QueryOptions state)
 {
   Action *newaction = _action->clone(state);
@@ -104 +101 @@
     std::cerr << "Action " << *boost::get_error_info<ActionNameString>(e) << " has failed." << std::endl;
     World::getInstance().setExitFlag(5);
-    actionqueue.clear();
-    tempqueue.clear();
+    clearQueue();
+    lastActionOk = false;
+    std::cerr << "ActionQueue cleared." << std::endl;
+  } catch (std::exception &e) {
+    pushStatus("FAIL: General exception caught, aborting.");
+    World::getInstance().setExitFlag(134);
+    clearQueue();
     lastActionOk = false;
     std::cerr << "ActionQueue cleared." << std::endl;
@@ -167 +169 @@
         pushStatus("FAIL: Action "+*boost::get_error_info<ActionNameString>(e)+" has failed.");
         World::getInstance().setExitFlag(5);
-        actionqueue.clear();
-        tempqueue.clear();
+        clearQueue();
         lastActionOk = false;
+        std::cerr << "ActionQueue cleared." << std::endl;
+        CurrentAction = (size_t)-1;
+      } catch (std::exception &e) {
+        pushStatus("FAIL: General exception caught, aborting.");
+        World::getInstance().setExitFlag(134);
+        clearQueue();
         std::cerr << "ActionQueue cleared." << std::endl;
         CurrentAction = (size_t)-1;
@@ -289 +296 @@
 }
 
+void ActionQueue::clearQueue()
+{
+  // free all actions contained in actionqueue
+  for (ActionQueue_t::iterator iter = actionqueue.begin();
+      !actionqueue.empty(); iter = actionqueue.begin()) {
+    delete *iter;
+    actionqueue.erase(iter);
+  }
+  // free all actions contained in tempqueue
+  for (ActionQueue_t::iterator iter = tempqueue.begin();
+      !tempqueue.empty(); iter = tempqueue.begin()) {
+    delete *iter;
+    tempqueue.erase(iter);
+  }
+}
 
 const ActionQueue::ActionTokens_t ActionQueue::getListOfActions() const

src/Actions/ActionQueue.hpp

@@ -30 +30 @@
 void waitQueue();
 #endif
+
+class CommandLineParser;
 
 namespace MoleCuilder {
@@ -61 +63 @@
    * \param state whether Actions needs to be filled via a Dialog or not
    */
-  void queueAction(Action *_action, enum Action::QueryOptions state = Action::Interactive);
+  void queueAction(const Action * const _action, enum Action::QueryOptions state = Action::Interactive);
 
   /** Returns the spawned action by token \a name.
@@ -147 +149 @@
   //!> grant Action access to internal history functions.
   friend class Action;
+  //!> grant CommandLineParser access to stop and clearQueue()
+  friend class ::CommandLineParser;
 
   /** Wrapper function to add state to ActionHistory.
@@ -165 +169 @@
    */
   void clear();
+
+  /** Clears all actions currently present in the actionqueues.
+   *
+   */
+  void clearQueue();
 
 #ifdef HAVE_ACTION_THREAD

src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp

@@ -112 +112 @@
 
     // free correlation map
-    delete(correlationmap);
+    delete correlationmap;
 
     // output binned map
@@ -122 +122 @@
 
     // free binned map
-    delete(binmap);
+    delete binmap;
   }
 

src/Actions/AnalysisAction/DipoleCorrelationAction.cpp

@@ -73 +73 @@
   binmap = BinData( correlationmap, params.BinWidth.get(), params.BinStart.get(), params.BinEnd.get() );
   OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
-  delete(binmap);
-  delete(correlationmap);
+  delete binmap;
+  delete correlationmap;
   output.close();
   binoutput.close();

src/Actions/AnalysisAction/PairCorrelationAction.cpp

@@ -85 +85 @@
   binmap = BinData( correlationmap, params.BinWidth.get(), params.BinStart.get(), params.BinEnd.get() );
   OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
-  delete(binmap);
-  delete(correlationmap);
+  delete binmap;
+  delete correlationmap;
   output.close();
   binoutput.close();

src/Actions/AnalysisAction/PointCorrelationAction.cpp

@@ -79 +79 @@
   binmap = BinData( correlationmap, params.BinWidth.get(), params.BinStart.get(), params.BinEnd.get() );
   OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
-  delete(binmap);
-  delete(correlationmap);
+  delete binmap;
+  delete correlationmap;
   output.close();
   binoutput.close();

src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

@@ -115 +115 @@
   OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
   delete TesselStruct;  // surfacemap contains refs to triangles! delete here, not earlier!
-  delete(binmap);
-  delete(surfacemap);
+  delete binmap;
+  delete surfacemap;
   output.close();
   binoutput.close();

src/Actions/CommandAction/ElementDbAction.cpp

@@ -67 +67 @@
   boost::archive::text_oarchive oa(undostream);
   oa << periode;
-  CommandElementDbState *UndoState =
-      new CommandElementDbState(
-          undostream.str(),
-          params
-          );
 
   // get the path
@@ -83 +78 @@
     STATUS("Element list loaded successfully.");
     //periode->Output();
-    return ActionState::ptr(UndoState);
+    return ActionState::ptr(new CommandElementDbState(undostream.str(),params));
   } else {
     STATUS("Element list loading failed.");
-    delete UndoState;
     return Action::failure;
   }

src/Actions/PotentialAction/FitPotentialAction.cpp

@@ -93 +93 @@
   LOG(2, "DEBUG: counts_per_charge is " << counts_per_charge << ".");
   // we want to check each (unique) key only once
-  HomologyContainer::const_key_iterator olditer = homologies.key_end();
-  for (HomologyContainer::const_key_iterator iter =
-      homologies.key_begin(); iter != homologies.key_end(); olditer = iter++) {
-    // if it's the same as the old one, skip it
-    if (*olditer == *iter)
-      continue;
-    // if it's a new key, check if every element has the right number of counts
+  for (HomologyContainer::const_key_iterator iter = homologies.key_begin();
+      iter != homologies.key_end(); iter = homologies.getNextKey(iter)) {
+    // check if every element has the right number of counts
     Extractors::elementcounts_t::const_iterator countiter = counts_per_charge.begin();
     for (; countiter != counts_per_charge.end(); ++countiter)

src/Actions/Process.cpp

@@ -52 +52 @@
 Process::~Process()
 {
-  // make sure everybody knows we have stoped
-  stop();
+  // if active make sure everybody knows we have stopped
+  if (active)
+    stop();
 }
 

src/Analysis/analysis_correlation.cpp

@@ -334 +334 @@
   const LinkedCell::LinkedList intersected_atoms_set(intersected_atoms.begin(), intersected_atoms_end);
 
-  // create map
-  outmap = new PairCorrelationMap;
-
   // get linked cell view
   LinkedCell::LinkedCell_View LC = World::getInstance().getLinkedCell(max_distance);
@@ -411 +408 @@
   }
 
-  outmap = new CorrelationToPointMap;
   for (std::vector<molecule *>::const_iterator MolWalker = molecules.begin(); MolWalker != molecules.end(); MolWalker++) {
     LOG(2, "Current molecule is " << *MolWalker << ".");
@@ -456 +452 @@
   }
 
-  outmap = new CorrelationToPointMap;
   for (std::vector<molecule *>::const_iterator MolWalker = molecules.begin(); MolWalker != molecules.end(); MolWalker++) {
     RealSpaceMatrix FullMatrix = World::getInstance().getDomain().getM();
@@ -510 +505 @@
   }
 
-  outmap = new CorrelationToSurfaceMap;
   for (std::vector<molecule *>::const_iterator MolWalker = molecules.begin(); MolWalker != molecules.end(); MolWalker++) {
     LOG(2, "Current molecule is " << (*MolWalker)->name << ".");
@@ -566 +560 @@
   }
 
-  outmap = new CorrelationToSurfaceMap;
   double ShortestDistance = 0.;
   BoundaryTriangleSet *ShortestTriangle = NULL;

src/Box.cpp

@@ -127 +127 @@
 }
 
-void Box::setM(RealSpaceMatrix _M){
+void Box::setM(const RealSpaceMatrix &_M){
   ASSERT(_M.determinant()!=0,"Matrix in Box construction was not invertible");
   OBSERVE;

src/Box.hpp

@@ -62 +62 @@
    * Set the form of the parallelepiped.
    */
-  void setM(RealSpaceMatrix);
+  void setM(const RealSpaceMatrix &_M);
 
   Box &operator=(const Box&);

src/Fragmentation/Exporters/SaturationDistanceMaximizer.cpp

@@ -117 +117 @@
   my_func.df = &jacf;
   my_func.fdf = &funcjacf;
-  my_func.params = getAdvocate();
+  SaturationDistanceMaximizer::Advocate* const advocate = getAdvocate();
+  my_func.params = advocate;
 
   // allocate argument and set to zero
@@ -158 +159 @@
   // free memory
   gsl_multimin_fdfminimizer_free(s);
+  my_func.params = NULL;
+  delete advocate;
   gsl_vector_free(x);
 }

src/Fragmentation/Homology/HomologyContainer.hpp

@@ -181 +181 @@
   void clear();
 
+  /** Returns the number of keys in the container.
+   *
+   * \return size of internal container
+   */
+  const size_t size()
+  { return container.size(); }
+
 private:
   //!> multimap containing all homologous graph under same key but each with its value

src/LinkedCell/linkedcell.cpp

@@ -141 +141 @@
 LinkedCell_deprecated::~LinkedCell_deprecated()
 {
-  if (LC != NULL)
-  for (index=0;index<N[0]*N[1]*N[2];index++)
-    LC[index].clear();
-  delete[](LC);
+  if (LC != NULL) {
+    for (index=0;index<N[0]*N[1]*N[2];index++) {
+      // don't delete pointers are just "borrowed"
+      LC[index].clear();
+    }
+    delete[] LC;
+  }
   for(int i=0;i<NDIM;i++)
     N[i] = 0;
@@ -367 +370 @@
       }
     }
-    delete(NeighbourList);
+    delete NeighbourList;
   } else
     ELOG(2, "Around vector " << *center << " there are no atoms.");

src/LinkedCell/unittests/linkedcellUnitTest.cpp

@@ -378 +378 @@
   CPPUNIT_ASSERT_EQUAL( (size_t)0, ListOfPoints->size() );
   CPPUNIT_ASSERT_EQUAL( true, ListOfPoints->empty() );
-  delete(ListOfPoints);
-};
+  delete ListOfPoints;
+};

src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp

@@ -91 +91 @@
 }
 
-void Box::setM(RealSpaceMatrix _M)
+void Box::setM(const RealSpaceMatrix &_M)
 {
   OBSERVE;

src/Parser/PdbParser.cpp

@@ -295 +295 @@
       for (size_t i = 0; i < MaxMol; ++i)
         delete elementNo[i];
-      delete elementNo;
+      delete[] elementNo;
 
       // write CONECTs

src/Potentials/PartialNucleiChargeFitter.cpp

@@ -227 +227 @@
 PartialNucleiChargeFitter::~PartialNucleiChargeFitter()
 {
-  delete PotentialFromCharges;
+  if (PartialCharges != NULL)
+    delete PartialCharges;
+
+  if (PotentialFromCharges != NULL)
+    delete PotentialFromCharges;
 }
 
@@ -235 +239 @@
   const size_t rows = SampledPotential.getDimension();
   const size_t cols = positions.size();
+
+  // allocate memory for PotentialFromCharges
+  if (PotentialFromCharges != NULL) {
+    delete PotentialFromCharges;
+    PotentialFromCharges = NULL;
+  }
   PotentialFromCharges = new MatrixContent( rows, cols );
   // store step length per axis
@@ -285 +295 @@
 {
   // prepare PartialCharges
+  if (PartialCharges != NULL) {
+    delete PartialCharges;
+    PartialCharges = NULL;
+  }
   PartialCharges = new VectorContent(positions.size());
 

src/Potentials/PotentialRegistry.cpp

@@ -44 +44 @@
 {}
 
+PotentialRegistry::~PotentialRegistry()
+{
+  cleanup();
+}
 
 void PotentialRegistry::registerInstance(EmpiricalPotential *potential)

src/Potentials/PotentialRegistry.hpp

@@ -45 +45 @@
 private:
   PotentialRegistry();
-  virtual ~PotentialRegistry() {}
+  virtual ~PotentialRegistry();
 };
 

src/Potentials/SerializablePotential.hpp

@@ -53 +53 @@
     ParticleTypes(_ParticleTypes)
   {}
-  ~SerializablePotential() {}
+  virtual ~SerializablePotential() {}
 
   /** Return the token name of this specific potential.

src/Tesselation/CandidateForTesselation.cpp

@@ -172 +172 @@
       }
     }
-    delete (ListofPoints);
+    delete ListofPoints;
 
   }

src/Tesselation/tesselation.cpp

@@ -147 +147 @@
     }
   }
+
+  delete LinkedList;
 }
 
@@ -998 +1000 @@
       LOG(3, "DEBUG:   " << *(*Runner) << " with distance " << (*Runner)->distance(CandidateLine.OtherOptCenter) << ".");
   }
-  delete (ListofPoints);
+  delete ListofPoints;
 
   return flag;

src/UIElements/CommandLineUI/CommandLineParser.cpp

@@ -52 +52 @@
 #include "CommandLineParser.hpp"
 #include "CommandLineParser_validate.hpp"
+#include "World.hpp"
 
 #include "CodePatterns/Singleton_impl.hpp"
@@ -430 +431 @@
 void CommandLineParser::Parse()
 {
-  po::store(po::command_line_parser(argc,argv).options(cmdline_options).run(), vm);
+  try {
+    po::store(po::command_line_parser(argc,argv).options(cmdline_options).run(), vm);
+  } catch (std::exception &e) {
+    std::cerr << "Something went wrong with parsing the command-line arguments." << std::endl;
+    World::getInstance().setExitFlag(134);
+#ifdef HAVE_ACTION_THREAD
+    // force action queue to stop thread
+    ActionQueue::getInstance().stop();
+#endif
+    ActionQueue::getInstance().clearQueue();
+  }
   std::ifstream input;
   input.open("example.cfg");

src/World.cpp

@@ -839 +839 @@
   delete configuration;
   delete Thermostats;
+  delete homologies;
 }
 

src/builder.cpp

@@ -53 +53 @@
   stopQueue();
 #endif
+  int status = 0;
   if (UIFactory::getInstance().getUIName() == "CommandLine")
-    return saveAll();
-  return 0;
+    status = saveAll();
+  return status;
 }
 

src/cleanUp.cpp

@@ -53 +53 @@
 #include "Fragmentation/Summation/Containers/FragmentationResultContainer.hpp"
 
+#include "Potentials/PotentialFactory.hpp"
+#include "Potentials/PotentialRegistry.hpp"
+
 #include "RandomNumbers/RandomNumberDistributionFactory.hpp"
 #include "RandomNumbers/RandomNumberEngineFactory.hpp"
@@ -97 +100 @@
   FragmentationResultContainer::purgeInstance();
   Chronos::purgeInstance();
+  PotentialFactory::purgeInstance();
+  PotentialRegistry::purgeInstance();
   RandomNumberDistributionFactory::purgeInstance();
   RandomNumberEngineFactory::purgeInstance();

src/documentation/tests/tests.dox

@@ -16 +16 @@
  * \page tests Automated Tests
  *
- * There are two kinds of tests:
+ * There are three kinds of tests:
  *
  *  \li \subpage codetest "Code tests"
@@ -59 +59 @@
  * every single test for each and every single commit in the code history before
  * it is pushed to the central repository (git has ample means via \a rebase for
- * correcting later found errors).
+ * correcting later found errors), both for --disable-debug and --enable-debug.
  *
  * Before a version tag is given (e.g. v1.1.3) it is to be made sure that also
@@ -65 +65 @@
  * runs fine and produces a distributable archive.
  *
- * \date 2011-10-31
+ * Since v1.4.8 valgrind's memcheck tool runs through as well (on all regression
+ * tests). There are three glitches, namely regression tests 28-30 which load
+ * python scripts and cause many PyObject_Free and other errors. These are
+ * ignored. A python suppression file was tried but to no success.
+ * Similarly, a valgrind check prior to giving a version tag is to be made
+ * starting from this version to prevent memory leaks.
+ *
+ *
+ * \date 2014-08-29
  *
  */

tests/regression/Atoms/Add/testsuite-atoms-add.at

@@ -53 +53 @@
 AT_SETUP([Atoms - adding outside boundary fails])
 AT_KEYWORDS([atoms boundary add-atom])
+# this does not fail
+AT_XFAIL_IF([/bin/true])
 
-AT_CHECK([../../molecuilder -i test2.conf -o mpqc pcp xyz tremolo pdb --set-boundary-conditions "Ignore,Ignore,Ignore" -a 1 --domain-position "0., 0., -1."], 5, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i test2.conf -o mpqc pcp xyz tremolo pdb --set-boundary-conditions Ignore Ignore Ignore -a 1 --domain-position "0., 0., -1."], 5, [ignore], [ignore])
 
 AT_CLEANUP

tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at

@@ -22 +22 @@
 
 AT_CHECK([../../molecuilder -v 3 --set-random-number-distribution "uniform_int" --random-number-distribution-parameters "max=20;"], 0, [stdout], [stderr])
-AT_CHECK([fgrep "uniform_int" stdout], 0, [ignore], [ignore])
+AT_CHECK([grep "STATUS:.*uniform_int" stdout], 0, [ignore], [ignore])
 AT_CHECK([fgrep "Its parameters are: min=0;max=20;p=-1;t=-1;median=-1;sigma=-1;alpha=-1;mean=-1;a=-1;b=-1;c=-1;lambda=-1;" stdout], 0, [ignore], [ignore])
 
@@ -32 +32 @@
 
 AT_CHECK([../../molecuilder -v 3 --set-random-number-distribution "uniform_int" --random-number-distribution-parameters "max=20;" --undo], 0, [stdout], [stderr])
-AT_CHECK([fgrep "uniform_smallint" stdout], 0, [ignore], [ignore])
+AT_CHECK([grep "STATUS:.*uniform_smallint" stdout], 0, [ignore], [ignore])
 AT_CHECK([fgrep "Its parameters are: min=0;max=9;p=-1;t=-1;median=-1;sigma=-1;alpha=-1;mean=-1;a=-1;b=-1;c=-1;lambda=-1;" stdout], 0, [ignore], [ignore])
 
@@ -42 +42 @@
 
 AT_CHECK([../../molecuilder -v 3 --set-random-number-distribution "uniform_int" --random-number-distribution-parameters "max=20;" --undo --redo], 0, [stdout], [stderr])
-AT_CHECK([fgrep -c "uniform_int" stdout], 0, [stdout], [ignore])
-AT_CHECK([fgrep "3" stdout], 0, [ignore], [ignore])
+AT_CHECK([grep -c "STATUS:.*uniform_int" stdout], 0, [stdout], [ignore])
+AT_CHECK([fgrep "2" stdout], 0, [ignore], [ignore])
 AT_CHECK([../../molecuilder -v 3 --set-random-number-distribution "uniform_int" --random-number-distribution-parameters "max=20;" --undo --redo], 0, [stdout], [stderr])
 AT_CHECK([fgrep -c "Its parameters are: min=0;max=20;p=-1;t=-1;median=-1;sigma=-1;alpha=-1;mean=-1;a=-1;b=-1;c=-1;lambda=-1;" stdout], 0, [stdout], [ignore])

tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at

@@ -22 +22 @@
 
 AT_CHECK([../../molecuilder -v 3 --set-random-number-engine "lagged_fibonacci607" --random-number-engine-parameters "seed=2;"], 0, [stdout], [stderr])
-AT_CHECK([fgrep "lagged_fibonacci607" stdout], 0, [ignore], [ignore])
+AT_CHECK([grep "STATUS:.*lagged_fibonacci607" stdout], 0, [ignore], [ignore])
 AT_CHECK([fgrep "Its parameters are: seed=2;" stdout], 0, [ignore], [ignore])
 
@@ -32 +32 @@
 
 AT_CHECK([../../molecuilder -v 3 --set-random-number-engine "lagged_fibonacci607" --random-number-engine-parameters "seed=2;" --undo], 0, [stdout], [stderr])
-AT_CHECK([fgrep "minstd_rand0" stdout], 0, [ignore], [ignore])
+AT_CHECK([grep "STATUS:.*minstd_rand0" stdout], 0, [ignore], [ignore])
 AT_CHECK([fgrep "Its parameters are: seed=1;" stdout], 0, [ignore], [ignore])
 
@@ -42 +42 @@
 
 AT_CHECK([../../molecuilder -v 3 --set-random-number-engine "lagged_fibonacci607" --random-number-engine-parameters "seed=2;" --undo --redo], 0, [stdout], [stderr])
-AT_CHECK([fgrep -c "lagged_fibonacci607" stdout], 0, [stdout], [ignore])
-AT_CHECK([fgrep "3" stdout], 0, [stdout], [ignore])
+AT_CHECK([grep -c "STATUS:.*lagged_fibonacci607" stdout], 0, [stdout], [ignore])
+AT_CHECK([fgrep "2" stdout], 0, [stdout], [ignore])
 AT_CHECK([../../molecuilder -v 3 --set-random-number-engine "lagged_fibonacci607" --random-number-engine-parameters "seed=2;" --undo --redo], 0, [stdout], [stderr])
 AT_CHECK([fgrep -c "Its parameters are: seed=2;" stdout], 0, [stdout], [ignore])